Restrict label demotion to chemicals only#725
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gaurav wants to merge 1 commit intoadd-pipeline-tests-for-shared-identifiersfrom
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Restrict label demotion to chemicals only#725gaurav wants to merge 1 commit intoadd-pipeline-tests-for-shared-identifiersfrom
gaurav wants to merge 1 commit intoadd-pipeline-tests-for-shared-identifiersfrom
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The previous config had a single global `demote_labels_longer_than: 25` that applied to every Biolink type. This caused legitimate disease and phenotype labels like "postural orthostatic tachycardia syndrome" and "Failure to thrive" to be dropped in favour of shorter, less informative alternatives from UMLS. Change `demote_labels_longer_than` to a per-type dict (same pattern as `preferred_name_boost_prefixes`). Only `biolink:ChemicalEntity: 25` is set, so demotion now applies only to chemicals and their subtypes via ancestor traversal. Types with no entry are never demoted. Extract the inline label-selection block from `write_compendium()` into a standalone `_select_preferred_label()` helper and add unit tests in `tests/babel_utils/test_write_compendia.py` with regression cases from the linked issues. Co-Authored-By: Claude Sonnet 4.6 <[email protected]>
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Drives write_compendium() against curated cliques and asserts on the JSONL output's preferred_name. Covers the regressions fixed in PR #725 (#711, #714, #723) and the chemical demotion path. Tests run offline by patching bmt.Toolkit to read pinned local Biolink Model files; a network freshness test fails loudly when the fixture and config.yaml's biolink_version drift apart. Co-Authored-By: Claude Opus 4.7 <[email protected]>
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The previous config had a single global
demote_labels_longer_than: 25that applied to every Biolink type. This caused legitimate disease and phenotype labels like "postural orthostatic tachycardia syndrome" and "Failure to thrive" to be dropped in favour of shorter, less informative alternatives from UMLS.Change
demote_labels_longer_thanto a per-type dict (same pattern aspreferred_name_boost_prefixes). Onlybiolink:ChemicalEntity: 25is set, so demotion now applies only to chemicals and their subtypes via ancestor traversal. Types with no entry are never demoted.Extract the inline label-selection block from
write_compendium()into a standalone_select_preferred_label()helper and add unit tests intests/babel_utils/test_write_compendia.pywith regression cases from the linked issues.Fixes #597, fixes #711, fixes #714, fixes #723